一种新模式识别方法在DNA序列分析中的应用：大肠杆菌启动子研究
Application of a new method of pattern recognition in DNA sequence analysis: a study of E. coli promoters.
作者信息
Alexandrov N N, Mironov A A
机构信息
Genetics of Microorganisms Institute, Moscow, USSR.
出版信息
Nucleic Acids Res. 1990 Apr 11;18(7):1847-52. doi: 10.1093/nar/18.7.1847.
Abstract
An algorithm from the pattern recognition theory 'generalized portrait' was used to find a distinguishing vector (scoring matrix) for E. coli promoters. We have attempted to solve three closely linked problems: (i) the selection of significant features of the signal; (ii) subsequent multiple alignment and (iii) calculation of the vector coordinates. Promoters with known strength have been successfully ranked in the correct order using this vector. We demonstrate the use of this method in predicting the location of promoters. A revised consensus promoter sequence is also presented.
摘要
运用模式识别理论“广义画像”中的一种算法来寻找大肠杆菌启动子的区分向量（评分矩阵）。我们试图解决三个紧密相关的问题：（i）信号显著特征的选择；（ii）随后的多序列比对；以及（iii）向量坐标的计算。利用该向量已成功地将已知强度的启动子按正确顺序进行了排序。我们展示了该方法在预测启动子位置方面的应用。还给出了一个修订后的共有启动子序列。
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2
A computer algorithm for testing potential prokaryotic terminators.一种用于测试潜在原核生物终止子的计算机算法。
Nucleic Acids Res. 1984 May 25;12(10):4411-27. doi: 10.1093/nar/12.10.4411.
3
Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity.大肠杆菌启动子序列可预测体外RNA聚合酶的选择性。
Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):789-800. doi: 10.1093/nar/12.1part2.789.
4
Computer methods to locate signals in nucleic acid sequences.在核酸序列中定位信号的计算机方法。
Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):505-19. doi: 10.1093/nar/12.1part2.505.
5
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Nucleic Acids Res. 1983 Apr 25;11(8):2237-55. doi: 10.1093/nar/11.8.2237.
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7
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8
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Comput Appl Biosci. 1987 Jun;3(2):93-8. doi: 10.1093/bioinformatics/3.2.93.
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